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. 2018 Sep 7:1:137.
doi: 10.1038/s42003-018-0141-4. eCollection 2018.

PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation

Julia Jehn  1 , Daniel Gebert  1 , Frank Pipilescu  1 , Sarah Stern  1 , Julian Simon Thilo Kiefer  1 , Charlotte Hewel  1 , David Rosenkranz  2
Affiliations

PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation

Julia Jehn et al. Commun Biol. .

Abstract

PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus protecting their genomes from detrimental insertion mutagenesis. Here, we reveal that PIWI genes and piRNAs are ubiquitously expressed in mollusks, similar to the situation in arthropods. We describe lineage-specific adaptations of transposon composition in piRNA clusters in the great pond snail and the pacific oyster, likely reflecting differential transposon activity in gastropods and bivalves. We further show that different piRNA clusters with unique transposon composition are dynamically expressed during oyster development. Finally, bioinformatics analyses suggest that different populations of piRNAs presumably bound to different PIWI paralogs participate in homotypic and heterotypic ping-pong amplification loops in a tissue- and sex-specific manner. Together with recent findings from other animal species, our results support the idea that somatic piRNA expression represents the ancestral state in metazoans.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Evolution and expression of PIWI genes in mollusks. a PIWI gene tree reconstruction of molluskan PIWI genes. b Control PCR with PIWI paralog specific primers and L. stagnalis cDNA from the reproductive tract. The complete gel is shown in Supplemental Fig. 1g. c qPCR results for PIWI paralog expression in different tissues of L. stagnalis, measured as n-fold expression of the housekeeping gene GPI. Center line indicates median, box limits represent the 50th percentile, whiskers show the upper and lower extremes. d PIWI paralog expression in different tissues of L. stagnalis, normalized by the expression of the housekeeping gene GPI, values from reproductive tract set to 1. Center line indicates median, box limits represent the 50th percentile, whiskers show the upper and lower extremes. e Control PCR with PIWI paralog specific primers and C. gigas cDNA from the adductor muscle. The complete gel is shown in Supplemental Fig. 1h. f qPCR results for PIWI paralog expression in different tissues of C. gigas, measured as n-fold expression of the housekeeping gene PPIA. Center line indicates median, box limits represent the 50th percentile, whiskers show the upper and lower extremes. g PIWI paralog expression in different tissues of C. gigas, normalized by the expression of the housekeeping gene PPIA, values from male gonad set to 1. Center line indicates median, box limits represent the 50th percentile, whiskers show the upper and lower extremes
Fig. 2
Fig. 2
Characterization of small RNAs from L. stagnalis (foot-) muscle and reproductive tract. a Sequence read length distribution of mapped (top) and unannotated (intergenic) reads (bottom). b Results from small RNA annotation with unitas (top) and transposon content of intergenic reads (bottom). c Ping-pong signature. P-values are deduced from the corresponding Z-scores. P-values for all reads and reads that match mRNA are shown. d Differential expression of 307 predicted piRNA clusters. Colors refer to expression relative to highest/lowest expression within one tissue. Dots indicate n-fold expression of a given cluster in reproductive tract relative to muscle. e Amount of clustered reads and ping-pong reads per million bootstrapped reads (ppr-mbr). f Representation of transposons in the genome of L. stagnalis, plotted by divergence [%] from transposon consensus. g Representation of transposons within piRNA clusters of L. stagnalis, plotted by divergence [%] from transposon consensus. h Prominent transposons that are enriched or depleted in L. stagnalis piRNA clusters
Fig. 3
Fig. 3
Characterization of small RNAs and piRNA clusters from different C. gigas samples. a Sequence reads without annotation produce a significant ping-pong signature (top row of bars, only Z-scores for 10 bp 5′ overlap are shown). The number of ping-pong reads per million bootstrapped reads (middle row of bars), and the number of clustered reads (bottom row of bars) differs considerably across the samples. Heatmap shows the differential expression of the top 100 piRNA clusters in terms of maximum rpm coverage. Different classes of piRNA clusters are expressed during oyster development and in adult somatic tissues (bottom). Error bars indicate standard deviation. b Transposon composition of piRNA clusters belonging to four different classes. c Representation of transposons in the genome of C. gigas, plotted by divergence [%] from transposon consensus. d Representation of transposons within piRNA clusters of C. gigas, plotted by divergence [%] from transposon consensus. e Prominent transposons that are enriched or depleted in C. gigas piRNA clusters
Fig. 4
Fig. 4
Analysis of piRNAs that participate in the ping-pong amplification loop. a Ping-pong matrices illustrate frequent length-combinations of ping-pong pairs (sequences with 10 bp 5′ overlap). Sequence read length distribution and 1U/10A bias [bits] for ping-pong sequences are shown. b Proposed model of ping-pong amplification in the germline and muscle of C. gigas and L. stagnalis
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